Development and Application of InDel Markers in Flowering Chinese Cabbage Based on RAD-seq

Abstract

【Objective】The study aimed to develop highly polymorphic InDel markers for molecular marker assisted breeding of flowering Chinese cabbage.【Method】The InDel loci were identified by comparing RAD-seq data from four flowering Chinese cabbage accessions with the genome sequence of Chiifu-401-42 as a reference. InDel loci with potential polymorphism were screened out among four accessions by using bioinformatics methods. From these, 80 InDel loci evenly distributed across 10 chromosomes were selected for primer design and genetic diversity of 55 flowering Chinese cabbage accessions were evaluated.【Result】By alignment with reference genome sequence, a total of 84 510 InDel loci were identified in RAD-seq data of four accessions. Among them, 3 609 InDel loci (> 5 bp) were possibly polymorphic among four flowering Chinese cabbage accessions. Of 80 InDel loci selected for PCR amplification validation, 58 (72.5%) InDel markers showed polymorphism in the four sequenced accessions, and 133 alleles were detected in 55 accessions. The polymorphic information content (PIC) of these 58 markers ranged from 0.263 to 0.618, with an average of 0.443. Based on the detection results of InDel markers, the genetic similarity coefficient of 55 accessions ranged from 0.366 to 0.756, with an average of 0.570. The 55 accessions were classified into four groups with a genetic similarity coefficient of 0.564, and no significant difference was found in heat resistance among different groups.【Conclusion】The nDel markers with good polymorphism developed in this study can effectively reveal the genetic distance among different flowering Chinese cabbage germplasm materials, which could provide useful marker information for genetic germplasm analysis and new variety breeding of flowering Chinese cabbage.

Keywords

• flowering chinese cabbage
• rad-seq
• indel marker
• polymorphism
• genetic diversity analysis
• cluster analysis